Peptides (version 1.1.2)

boman: Compute the Boman (Potential Protein Interaction) index

Description

This function computes the potential protein interaction index proposed by Boman (2003) based in the amino acid sequence of a protein. The index is equal to the sum of the solubility values for all residues in a sequence, it might give an overall estimate of the potential of a peptide to bind to membranes or other proteins as receptors, to normalize it is divided by the number of residues. A protein have high binding potential if the index value is higher than 2.48.

Usage

boman(seq)

Arguments

seq

aminoacid sequence string

References

Boman, H. G. (2003). Antibacterial peptides: basic facts and emerging concepts. Journal of internal medicine, 254(3), 197-215.

Radzicka, A., & Wolfenden, R. (1988). Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry, 27(5), 1664-1670.

Examples

# COMPARED TO YADAMP DATABASE
# http://yadamp.unisa.it/showItem.aspx?yadampid=845&x=0,4373912
# SEQUENCE: FLPVLAGLTPSIVPKLVCLLTKKC
# BOMAN INDEX  -1.24  

boman("FLPVLAGLTPSIVPKLVCLLTKKC")
# [1] -1.235833